def test23CheckNonProduct(self):
smirks_thiourea = "[N;$(N-[#6]):3]=[C;$(C=S):1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);!$([ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[N:3]-[C:1]-[N+0:2]"
rxn = rdChemReactions.ReactionFromSmarts(smirks_thiourea)
mol = Chem.MolFromSmiles("CCCCCCCC")
m = rdChemReactions.ReduceProductToSideChains(mol)
self.assertTrue(m.GetNumAtoms() == 0)
mol = Chem.AddHs(mol)
m = rdChemReactions.ReduceProductToSideChains(mol)
self.assertTrue(m.GetNumAtoms() == 0)
def test22RunSingleReactant(self):
# from
# A Collection of Robust Organic Synthesis Reactions for In Silico Molecule Design
# Markus Hartenfeller,*, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber,
# Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, and Steffen Renner
# Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1,
# Novartis Campus, CH-4056 Basel, Switzerland Swiss Federal Institute of Technology (ETH)
# Zurich, Switzerland
smirks_thiourea = "[N;$(N-[#6]):3]=[C;$(C=S):1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);!$([ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[N:3]-[C:1]-[N+0:2]"
rxn = rdChemReactions.ReactionFromSmarts(smirks_thiourea)
reagents = [
Chem.MolFromSmiles(x) for x in ['C=CCN=C=S', 'NCc1ncc(Cl)cc1Br']
]
res = rxn.RunReactants(reagents)
self.assertTrue(res)
expected_result = [Chem.MolToSmiles(Chem.MolFromSmiles("C=CCNC(N)=S"))]
expected_result.sort()
sidechains_expected_result = [
Chem.MolToSmiles(Chem.MolFromSmiles("[*:1]=S.[*:3]CC=C"),
isomericSmiles=True)
]
sidechains_nodummy_expected_result = [[0, [
3,
], [
1,
]], [3, [
1,
], [
2,
]]]
sidechains_nodummy = []
sidechains_expected_result.sort()
for addDummy in [True, False]:
res = rxn.RunReactant(reagents[0], 0)
assert res
result = []
sidechains = []
for match in res:
for mol in match:
result.append(Chem.MolToSmiles(mol, isomericSmiles=True))
sidechain = rdChemReactions.ReduceProductToSideChains(
mol, addDummy)
sidechains.append(
Chem.MolToSmiles(sidechain, isomericSmiles=True))
if not addDummy:
for atom in sidechain.GetAtoms():
if atom.HasProp("_rgroupAtomMaps"):
sidechains_nodummy.append([
atom.GetIdx(),
eval(atom.GetProp("_rgroupAtomMaps")),
eval(atom.GetProp("_rgroupBonds")),
])
result.sort()
sidechains.sort()
if addDummy:
self.assertEquals(result, expected_result)
self.assertEquals(sidechains, sidechains_expected_result)
else:
self.assertEquals(sidechains_nodummy,
sidechains_nodummy_expected_result)
expected_result = [
Chem.MolToSmiles(Chem.MolFromSmiles("NCNCc1ncc(Cl)cc1Br"))
]
expected_result.sort()
sidechains_expected_result = [
Chem.MolToSmiles(Chem.MolFromSmiles("[*:2]Cc1ncc(Cl)cc1Br"),
isomericSmiles=True)
]
sidechains_expected_result.sort()
res = rxn.RunReactant(reagents[1], 1)
result = []
sidechains = []
for match in res:
for mol in match:
result.append(Chem.MolToSmiles(mol, isomericSmiles=True))
sidechains.append(
Chem.MolToSmiles(
rdChemReactions.ReduceProductToSideChains(mol),
isomericSmiles=True))
result.sort()
self.assertEquals(result, expected_result)
self.assertEquals(sidechains, sidechains_expected_result)
self.assertFalse(rxn.RunReactant(reagents[0], 1))
self.assertFalse(rxn.RunReactant(reagents[1], 0))
# try a broken ring based side-chain
sidechains_expected_result = ['c1ccc2c(c1)nc1n2CC[*:2]1']
reactant = Chem.MolFromSmiles('c1ccc2c(c1)nc1n2CCN1')
res = rxn.RunReactant(reactant, 1)
result = []
sidechains = []
for match in res:
for mol in match:
result.append(Chem.MolToSmiles(mol, isomericSmiles=True))
sidechains.append(
Chem.MolToSmiles(
rdChemReactions.ReduceProductToSideChains(mol),
isomericSmiles=True))
sidechain = rdChemReactions.ReduceProductToSideChains(
mol, addDummyAtoms=False)
self.assertEquals(sidechains, sidechains_expected_result)
